Heading time stability is essential for stable production of barley under the recent changes in climate. In this study we sought to identify QTLs regulating heading time and stability, using RILs derived from a cross between two Japanese cultivars, Kashimamugi and Ishukushirazu, both of which are early heading cultivars with spring growth habit, but differ in heading time stability. QTL analysis was performed by detecting genome-wide SNPs and InDels by MIG-seq, and detected three heading time QTLs ( QHd.ouj-2H, QHd.ouj-4H, and QHd.ouj-5H). Among these, HvCEN and HvPHYC were considered to be the causative genes for QHd.ouj-2H and QHd.ouj-5H, respectively, while the gene underlying QHd.ouj-4H remains unknown. QTL analysis failed to detect QTLs for heading time stability, but analysis of the three heading time QTLs revealed that heading time stability was affected by the HvPHYC genotype with an early allele causing instability. In addition, the effect of HvPHYC varied depending on the QHd.ouj-4H genotype, indicating interaction between HvPHYC and QHd.ouj-4H in which an early allele of QHd.ouj-4H suppresses heading time instability caused by an early allele of HvPHYC. Since early-maturing cultivars are widely cultivated to avoid abiotic stresses, these results facilitate the breeding of barley cultivars under the changing global climate.